tmm_r <- read.delim(file = "mate_00vs02_tmm_filt_annot.txt", header=TRUE, row.names = NULL, com='', check.names=F)
head(tmm_r)
##     locus_tag   X00_mean   X02_mean      theta      prob     log2FC length.x
## 1 HVO_RS00090   57.83890   31.14313  0.6374613 0.9297680  0.8931261      653
## 2 HVO_RS00350   35.65117   58.33130 -0.3730532 0.7434937 -0.7103209      530
## 3 HVO_RS00570   62.16598   27.22173  0.9027281 0.9843431  1.1913668     1949
## 4 HVO_RS00635   45.59738   29.56472  0.4659552 0.8913868  0.6250740      863
## 5 HVO_RS00705   38.48181   51.32470 -0.2878642 0.6195012 -0.4154764      695
## 6 HVO_RS00755 2358.10620 1036.62999  1.6725932 0.9999403  1.1857277      413
##              P             wp   dbxref                                ncbi_id
## 1 7.023204e-02 WP_004041134.1  8919107 lcl|NC_013964.1_cds_WP_004041134.1_106
## 2 2.565063e-01 WP_004041082.1  8919049 lcl|NC_013964.1_cds_WP_004041082.1_159
## 3 1.565688e-02 WP_004041038.1  8919024 lcl|NC_013964.1_cds_WP_004041038.1_203
## 4 1.086132e-01 WP_004041025.1  8919172 lcl|NC_013964.1_cds_WP_004041025.1_216
## 5 3.804988e-01 WP_004041011.1  8919253 lcl|NC_013964.1_cds_WP_004041011.1_230
## 6 5.971975e-05 WP_004041383.1 25143363 lcl|NC_013964.1_cds_WP_004041383.1_240
##   genomic_accession feature  start   stop strand gene gbkey   gene_biotype
## 1       NC_013964.1    gene  20051  20704      +  105  Gene protein_coding
## 2       NC_013964.1    gene  81961  82491      -  158  Gene protein_coding
## 3       NC_013964.1    gene 131561 133510      +  202  Gene protein_coding
## 4       NC_013964.1    gene 145516 146379      +  215  Gene protein_coding
## 5       NC_013964.1    gene 162589 163284      -  229  Gene protein_coding
## 6       NC_013964.1    gene 174818 175231      -  239  Gene protein_coding
##   old_locus_tag length.y                   protein kegg1 kegg2 kegg3 pathway
## 1     HVO_B0020      653  bacterio-opsin activator  <NA>  <NA>  <NA>    <NA>
## 2     HVO_B0073      530 transcriptional regulator  <NA>  <NA>  <NA>    <NA>
## 3     HVO_B0118     1949     SMC-like protein Sph2  <NA>  <NA>  <NA>    <NA>
## 4     HVO_B0131      863      hypothetical protein  <NA>  <NA>  <NA>    <NA>
## 5     HVO_B0145      695              creatininase  <NA>  <NA>  <NA>    <NA>
## 6   HVO_RS00755      413        response regulator  <NA>  <NA>  <NA>    <NA>
##   kegg_prot kegg_id definition keggidprot
## 1      <NA>    <NA>       <NA>     NA: NA
## 2      <NA>    <NA>       <NA>     NA: NA
## 3      <NA>    <NA>       <NA>     NA: NA
## 4      <NA>    <NA>       <NA>     NA: NA
## 5      <NA>    <NA>       <NA>     NA: NA
## 6      <NA>    <NA>       <NA>     NA: NA
##                                Gene.Name                Species EC_NUMBER
## 1  bacterio-opsin activator(HVO_RS00090) Haloferax volcanii DS2          
## 2 transcriptional regulator(HVO_RS00350) Haloferax volcanii DS2          
## 3     SMC-like protein Sph2(HVO_RS00570) Haloferax volcanii DS2          
## 4      hypothetical protein(HVO_RS00635) Haloferax volcanii DS2          
## 5              creatininase(HVO_RS00705) Haloferax volcanii DS2  3.5.2.10
## 6        response regulator(HVO_RS00755) Haloferax volcanii DS2          
##                                     GOTERM_BP_DIRECT         GOTERM_CC_DIRECT
## 1                                                                            
## 2            GO:0006351~transcription, DNA-templated GO:0005622~intracellular
## 3                                                                            
## 4                                                                            
## 5                                                                            
## 6 GO:0000160~phosphorelay signal transduction system GO:0005622~intracellular
##                                                                                                   GOTERM_MF_DIRECT
## 1                                                                                                                 
## 2 GO:0003700~transcription factor activity, sequence-specific DNA binding,GO:0043565~sequence-specific DNA binding
## 3                                                                                                                 
## 4                                                                                                                 
## 5                                                                                 GO:0047789~creatininase activity
## 6                                                                                       GO:0016301~kinase activity
##                                                                                                                          INTERPRO
## 1                                                                            IPR007050:Transcription regulator HTH, bacterioopsin
## 2 IPR000485:AsnC-type HTH domain,IPR011991:Winged helix-turn-helix DNA-binding domain,IPR019888:Transcription regulator AsnC-type
## 3                                                                   IPR027417:P-loop containing nucleoside triphosphate hydrolase
## 4                                                                            IPR011991:Winged helix-turn-helix DNA-binding domain
## 5                                                   IPR003785:Creatininase/formamide hydrolase,IPR024087:Creatininase-like domain
## 6                               IPR001789:Signal transduction response regulator, receiver domain,IPR011006:CheY-like superfamily
##   KEGG_PATHWAY OFFICIAL_GENE_SYMBOL                                       PFAM
## 1                       HVO_RS00090             PF04967:HTH DNA binding domain
## 2                       HVO_RS00350  PF13404:AsnC-type helix-turn-helix domain
## 3                       HVO_RS00570                                           
## 4                       HVO_RS00635                                           
## 5                       HVO_RS00705          PF02633:Creatinine amidohydrolase
## 6                       HVO_RS00755 PF00072:Response regulator receiver domain
##   PIR_SUPERFAMILY            SMART
## 1                                 
## 2                 SM00344:HTH_ASNC
## 3                                 
## 4                                 
## 5                                 
## 6                      SM00448:REC
##                                                                                        UP_KEYWORDS
## 1                                                    Complete proteome,Plasmid,Reference proteome,
## 2 Complete proteome,DNA-binding,Plasmid,Reference proteome,Transcription,Transcription regulation,
## 3                                                                   Coiled coil,Complete proteome,
## 4                                                    Complete proteome,Plasmid,Reference proteome,
## 5                                          Complete proteome,Hydrolase,Plasmid,Reference proteome,
## 6                                                            Complete proteome,Kinase,Transferase,
##    chr arCOG_name E.value score arCOG_familiy Gene_name
## 1 pHV3 arCOG02276 1.4e-21  75.5             T         -
## 2 pHV3 arCOG01587 2.6e-64 213.6             K         -
## 3 pHV3 arCOG00385 2.0e-08  32.2             S         -
## 4 pHV3 arCOG01449 2.3e-66 221.6             V      Csx1
## 5 pHV3 arCOG04536 2.6e-46 155.7             H      ArfB
## 6 pHV3 arCOG02595 1.1e-33 113.2             T      OmpR
##                                                                                                   Description
## 1                                                  Signal transduction regulator, containsPAS and HTH domains
## 2                                                           DNA-binding transcriptional regulator, Lrp family
## 3                                                                         Uncharacterized coiled-coil protein
## 4                                                                              CARF domain containing protein
## 5 Creatinine amidohydrolase/Fe(II)-dependent formamide hydrolase involved in riboflavin and F420 biosynthesis
## 6                                                                                                  REC domain
##         HVO EFFECTSIZE
## 1 HVO_B0020  0.8931261
## 2 HVO_B0073 -0.7103209
## 3 HVO_B0118  1.1913668
## 4 HVO_B0131  0.6250740
## 5 HVO_B0145 -0.4154764
## 6       ---  1.1857277
volc_obj <- volcanor(tmm_r, p = "P", effect_size = "EFFECTSIZE", snp = "locus_tag", 
                     gene = "protein", annotation1 = "old_locus_tag", annotation2 = "arCOG_name")
volc_plot <- volcanoly(volc_obj, effect_size_line = c(-3,3), effect_size_line_color = "orange", 
          genomewideline = -log10(1e-2), genomewideline_color = "green", title = "t00 vs t02")
volc_plot_fixed <- volcanoly(volc_obj, effect_size_line = c(-3,3), effect_size_line_color = "orange", 
          genomewideline = -log10(1e-2), genomewideline_color = "green", title = "t00 vs t02", 
          highlight = tmm_r$locus_tag, highlight_color = "black")
volcanoly(volc_obj, effect_size_line = c(-3,3), effect_size_line_color = "orange", 
          genomewideline = -log10(1e-2), genomewideline_color = "green", title = "t00 vs t02")

Volcano plot doesn’t have annotations for non-significant points

volcanoly(volc_obj, effect_size_line = c(-3,3), effect_size_line_color = "orange", 
          genomewideline = -log10(1e-2), genomewideline_color = "green", title = "t00 vs t02", 
          highlight = tmm_r$locus_tag, highlight_color = "black")

Annotations present for all, but significant are no longer separately highlighted

library(ggplot2)
library(plotly)
## 
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
## 
##     last_plot
## The following object is masked from 'package:stats':
## 
##     filter
## The following object is masked from 'package:graphics':
## 
##     layout
p <- ggplot(tmm_r) +
  geom_point(data = tmm_r, aes(x = log2FC, y = -log10(P), text = paste(locus_tag,"\n",protein,"\n",arCOG_name,"\n",old_locus_tag)),
             color = "black", cex = 2) +
#  geom_point(data = tmm_r, aes(x = log2FC, y = P), color = "lightgreen", cex = 3) +
  # geom_point(data = dfm1, aes(x = logFC.x, y = logFDR.x), color = "blue", cex = 3) +
  # geom_text(data = dfm1, aes(x = logFC.x, y = logFDR.x, label = gene), hjust = 1, vjust = 2) +
  theme_bw() +
  xlab("log(2) fold change") +
  ylab("log(10) FDR") +
  geom_vline(xintercept = 2, col = "red", linetype = "dashed", size = 0.5) +
  geom_vline(xintercept = -2, col = "red", linetype = "dashed", size = 0.5) +
  geom_hline(yintercept = 0.05, col = "red", linetype = "dashed", size = 0.5)
## Warning: Ignoring unknown aesthetics: text
p

ggplotly(p, tooltip = "text")